How Physiologic Targets Can Be Distinguished from Drug-Binding Proteins

Abstract

Some drugs in clinical trial owe their effectiveness to "off-target" activity. This and other observations raise a possibility that many studies to identify targets of drugs are incomplete. If "off-target" proteins are pharmacologically important it will be worthwhile to identify them early in the development process, for a better understanding of the molecular basis of drug action. Herein, we outline a multidisciplinary strategy for systematic identification of physiological targets of drugs in cells. A drugbinding protein whose genetic disruption yields very similar molecular effects as treatment of cells with the drug may be defined as a physiological target of the drug. For a drug developed with a "rational approach", it is desirable to verify experimentally that a protein used for hit optimization in vitro remains the sole polypeptide recognized by the drug in a cell.

Physiologic Targets and Modes of Action for CBL0137, a Lead for Human African Trypanosomiasis Drug Development

“…In pursuit of physiologic targets of the drug, trypanosome genes encoding CBL0137-binding proteins were knocked down, and resulting molecular effects were compared with those obtained after perturbation of trypanosomes with the drug (Meyer and Shapiro, 2021). For physiologic targets of the drug, the expectation was that molecular defects determined after their knockdown would be very similar to those obtained after adding CBL0137 to trypanosomes (Mensa-Wilmot, 2021).…”

Arsinothricin Inhibits Plasmodium falciparum Proliferation in Blood and Blocks Parasite Transmission to Mosquitoes

“…Thus, AST may have other target(s) besides PfGS-I. Effective drugs often have multiple targets [ 71 ], as represented by the front-line antimalarial artemisinin [ 72 ].…”

Hypothesis-generating proteome perturbation to identify NEU-4438 and acoziborole modes of action in the African Trypanosome

“…Differences in modes of action of NEU-4438 and SCYX-7158 imply that adding the former compound to small molecules in development for HAT chemotherapy is justifiable ( Figure S4 ). Knowledge of modes of molecular action is important for the identification of “physiologic targets” of a drug ( Mensa-Wilmot, 2021 ). So, our future work will include the discovery of NEU-4438-binding proteins whose genetic knockdown (or overexpression) may impede G1/S transition or prevent Tf endocytosis in T. brucei as demonstrated in this work ( Meyer and Shapiro, 2021 ).…”

“…As drugs can bind multiple proteins ( Bolognesi, 2013 ; Hafner et al., 2019 ), and a single binding pocket on a protein can bind more than one ligand ( Cerisier et al., 2019 ), discovery of physiologic drug targets is not a trivial undertaking ( Kubota et al., 2019 ). Many drug-binding proteins are not physiological targets which may be defined as proteins whose genetic disruption yields similar modes of action as the treatment of cells with the drug ( Mensa-Wilmot, 2021 ). Recent efforts to address the topic systematically with multi-disciplinary experimental approaches hold promise ( Meyer and Shapiro, 2021 ; Sanz-Rodriguez et al., 2022 ).…”

“…Modes of action for drugs discovered by target-based approaches are presumed to arise from the engagement of a known target in cells. In many cases, this assumption of a single drug target per cell has been challenged ( Cataldi et al., 2004 ; Chou et al., 2015 ; Dai et al., 2008 ; Davis et al., 2011 ; Dolloff et al., 2011 ; Dunne et al., 2011 ; Hafner et al., 2019 ; Jia et al., 2008 ; Karaman et al., 2008 ; Lackey, 2006 ; Larsson et al., 2012 ), implying that mechanistic studies focusing on one presumed target may need to be revisited (reviewed in ( Mensa-Wilmot, 2021 )). In the case of drugs developed by phenotypic screening, as has occurred frequently in anti-trypanosome chemotherapy ( Jacobs et al., 2011b ; Tarral et al., 2014 ), targets are not known.…”